The Portuguese boss felt the midfielder's reaction to being an unused substitute was completely natural as his side wrapped up their Group J campaign
Jose Mourinho admitted that Dele Alli is "not a happy player" after the Tottenham star left the bench during a Europa League win over Antwerp.
Tottenham secured top spot in Group J by earning a 2-0 home win over Antwerp on Thursday night.
Benfica loanee Carlos Vinicius opened the scoring just before the hour mark for the hosts when he tapped home from close range after Alireza Beiranvand spilled a brilliantly struck Gareth Bale free-kick.
Giovani Lo Celso doubled Spurs' advantage in the 71st minute, producing a cool finish after latching onto a perfectly weighted Harry Kane through ball in the opposition penalty area.
Mourinho's men held on for a victory which should ensure that they get a favourable draw in the Round of 32, but Alli endured another frustrating night on the sidelines.
Although Tottenham's head coach made full use of the five substitutions rule over the course of the match, he opted against handing the England international some much needed minutes on the continental stage.
Alli was seen storming down the tunnel after Mourinho made his final change, but he did return a short while later, with the Portuguese tactician ultimately unconcerned by his natural reaction.
"Let's not run away from reality," Mourinho told reporters of Alli post-match. "A player on the bench who realises all five subs have been used of course is not a happy player and I would not expect him to be happy."
Harry Winks also appeared to head to the changing rooms in a sulk after coming off for Tanguy Ndombele on 59 minutes, but Mourinho says he instructed the midfielder to go inside for warmth.
"I told him to go, I told every player that left the pitch to go because when the weather is cold I prefer they go to the dressing room and have a shower," he said. "I told them to go, some prefer to stay.
"Winks decided to go and I am happy with that because I am the one that told him to do it."
Mourinho added on his team's latest performance in Europe and the difficult juggling act he has on his hands with a large squad to choose from: "The game is open, when I thought about the changes the result was 0-0 then we scored a goal but that didn't change my mind.
"We needed a little bit more of routines which these players (Harry Kane, Son Heung-min and Tanguy Ndombele) have, and the intensity. They had the intensity because they play week in week out. We managed to keep Antwerp away from our goal. Joe Hart didn't make a single save. 0-0 at half time - I thought in the second half with bit of intensity they will collapse.
"It was a great free kick from Gareth Bale and a striker smelling the second ball to score. The decision was made. Harry is Harry and Sonny is intense.
"I can't keep the [whole] squad happy. I believe they are happy because we are winning but they're not happy because they're not playing."